There's no reason to believe that the second round of science would still arrive at earlier theories such as the pudding model of the atom.

That was very much a part of science. But it isn't any longer as a result of experimental evidence.

So your rebuttal glosses over the many failed scientific theories but then uses the failed religious ideas to invalidate any religious ideas.

When in truth, both science and religion have historically attempted to explain the unexplained. The methodology of science is much better, but they have both had many examples of dumb ideas in retrospect.

The reason why the Naassenes had such interesting ideas was that they ended up having incorporated the ideas of Leucretius, who in 50 BCE had written the only extant work from antiquity to describe survival of the fittest in detail.

At the time, there was no experimental evidence to support or falsify such theories. But at the time a religious group working on extrapolating theories built on top of naturalism ended up landing on very similar ideas to what we currently come up with having experimentally landed on evolutionary theory and having turned Plato's eventual creator of worlds (another philosophical influence on the Naassenes) from theory to practice.

So while science is more likely to be right more often as a result of far better methodology, the problem with the quote is that it's a "heuristic that almost always works" and fails to consider the edge cases when religious thought had attached itself to natural explanations which later turned out to be correct.

Effectively, any ideas predicated on concepts which will eventually be experimentally validated should be expected to arise again even after erasing earlier theorizing, as it's the replicability of experimental results that drives that reproduction. And any ideas, whether a part of science or outside of it, which are predicated on eventually falsified ideas have no guarantee of reproduction.

The mistake the quote embodies is the assumption that it's impossible for theological ideas to have attached themselves to experimentally reproducible concepts. But that has happened before, and it meant that the extrapolated theological concepts were also reproduced.

And that's to say nothing for the many reproduced beliefs on other reproducible foundations such as dying and rising gods or katabasis that occurred in completely separate communities. In those cases it was a result of watching the stars and observing the orbit of Venus dropping down below the ground to arise again days later. So you had a central American God navigating the underworld and resurrecting the dead associated with Venus independent and parallel to Ianna in the Mediterranean navigating the underworld and associated with Venus. Or the common beliefs about the immortality of snakes because of their shedding.

The quote is the kind of thing that seems clever but is factually incorrect and betrays the one offering it up as uninformed of what they are talking about despite their self-assuredness in borrowed pithiness.